new_timings.py

import gzip
import os
import random
import sys
import time

import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.RDLogger import logger

dname = os.path.dirname(__file__)


def data(fname):
  return os.path.join(dname, '..', 'Data', fname)


logger = logger()

tests = [1] * 1001
if len(sys.argv) > 1:
  tests = [0] * 1001
  for x in sys.argv[1:]:
    x = int(x)
    tests[x] = 1
ts = []
mols = []

if tests[0]:
  lines = gzip.open(data('znp.50k.smi.gz'), 'rt').readlines()
  logger.info('mols from smiles')
  nMols = 0
  nBad = 0
  t1 = time.time()
  for line in lines:
    line = line.strip().split(' ')
    m = Chem.MolFromSmiles(line[0])
    if m:
      nMols += 1
      mols.append(m)
    else:
      nBad += 1

  t2 = time.time()
  logger.info('Results1: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
  ts.append(t2 - t1)

if tests[1]:
  logger.info('Writing: Canonical SMILES')
  t1 = time.time()
  for mol in mols:
    smi = Chem.MolToSmiles(mol, True)
  t2 = time.time()
  logger.info('Results2: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[2]:
  sdData = gzip.open(data('mols.1000.sdf.gz'), 'rb').read()
  logger.info('mols from sdf')
  suppl = Chem.SDMolSupplier()
  suppl.SetData(sdData)
  nMols = 0
  nBad = 0
  t1 = time.time()
  for i in range(10):
    for m in suppl:
      if m:
        nMols += 1
        # mols.append(m)
      else:
        nBad += 1
  t2 = time.time()
  logger.info('Results1: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
  ts.append(t2 - t1)

if tests[3] or tests[4] or tests[5]:
  pattData = gzip.open(data('queries.txt.gz'), 'rt').readlines()
  pattData = [x.strip().replace('[H]', '').replace('()', '') for x in pattData]
  logger.info('patterns from smiles')
  patts = []
  nMols = 0
  t1 = time.time()
  for line in pattData:
    m = Chem.MolFromSmarts(line)
    if m:
      nMols += 1
      patts.append(m)
    else:
      nBad += 1
  t2 = time.time()
  logger.info('Results3: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
  ts.append(t2 - t1)
  random.seed(23)
  random.shuffle(patts)
  patts = patts[:100]

if tests[4]:
  logger.info('Matching1: HasSubstructMatch')
  t1 = time.time()
  for mol in mols:
    for patt in patts:
      mol.HasSubstructMatch(patt)
  t2 = time.time()
  logger.info('Results4: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[5]:
  logger.info('Matching2: GetSubstructMatches')
  t1 = time.time()
  for mol in mols:
    for patt in patts:
      mol.GetSubstructMatches(patt)
  t2 = time.time()
  logger.info('Results5: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[6] or tests[7] or tests[8]:
  logger.info('reading SMARTS')
  patts = []
  t1 = time.time()
  for line in open(data('RLewis_smarts.txt')):
    line = line.strip()
    if line == '' or line[0] == '#':
      continue
    splitL = line.split(' ')
    sma = splitL[0]
    m = Chem.MolFromSmarts(sma)
    if m:
      patts.append(m)
  t2 = time.time()
  logger.info('Results6: %.2f seconds for %d patterns' % (t2 - t1, len(patts)))
  ts.append(t2 - t1)

if tests[7]:
  logger.info('Matching3: HasSubstructMatch')
  t1 = time.time()
  for mol in mols:
    for patt in patts:
      mol.HasSubstructMatch(patt)
  t2 = time.time()
  logger.info('Results7: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[8]:
  logger.info('Matching4: GetSubstructMatches')
  t1 = time.time()
  for mol in mols:
    for patt in patts:
      mol.GetSubstructMatches(patt)
  t2 = time.time()
  logger.info('Results8: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[9]:
  logger.info('Writing: Mol blocks')
  t1 = time.time()
  for mol in mols:
    mb = Chem.MolToMolBlock(mol)
  t2 = time.time()
  logger.info('Results10: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[10]:
  from rdkit.Chem import BRICS
  logger.info('BRICS decomposition')
  t1 = time.time()
  for mol in mols:
    d = BRICS.BreakBRICSBonds(mol)
  t2 = time.time()
  logger.info('Results11: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[11]:
  logger.info('Generate 2D coords')
  t1 = time.time()
  for mol in mols:
    AllChem.Compute2DCoords(mol)
  t2 = time.time()
  logger.info('Results12: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[12]:
  logger.info('Generate topological fingerprints')
  t1 = time.time()
  for mol in mols:
    Chem.RDKFingerprint(mol)
  t2 = time.time()
  logger.info('Results16: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[13]:
  logger.info('Generate morgan fingerprints')
  t1 = time.time()
  for mol in mols:
    AllChem.GetMorganFingerprint(mol, radius=2)
  t2 = time.time()
  logger.info('Results16: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

print(f"| {rdkit.__version__} | {' | '.join(['%.1f' % x for x in ts])} |")